{"action":"created","issue":{"url":"https://api.github.com/repos/vibansal/HapCUT2/issues/8","repository_url":"https://api.github.com/repos/vibansal/HapCUT2","labels_url":"https://api.github.com/repos/vibansal/HapCUT2/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/vibansal/HapCUT2/issues/8/comments","events_url":"https://api.github.com/repos/vibansal/HapCUT2/issues/8/events","html_url":"https://github.com/vibansal/HapCUT2/issues/8","id":231441107,"number":8,"title":"Errors extracting reads covering heterozygous SNPs?","user":{"login":"yjqiu","id":5383918,"avatar_url":"https://avatars1.githubusercontent.com/u/5383918?v=3","gravatar_id":"","url":"https://api.github.com/users/yjqiu","html_url":"https://github.com/yjqiu","followers_url":"https://api.github.com/users/yjqiu/followers","following_url":"https://api.github.com/users/yjqiu/following{/other_user}","gists_url":"https://api.github.com/users/yjqiu/gists{/gist_id}","starred_url":"https://api.github.com/users/yjqiu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yjqiu/subscriptions","organizations_url":"https://api.github.com/users/yjqiu/orgs","repos_url":"https://api.github.com/users/yjqiu/repos","events_url":"https://api.github.com/users/yjqiu/events{/privacy}","received_events_url":"https://api.github.com/users/yjqiu/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-05-25T19:52:53Z","updated_at":"2017-05-25T23:58:34Z","closed_at":null,"body":"I am using extracHAIRS to get reads covering heterozygous SNPs. However, the SNPs seems to be ignored when two ends are overlapping. And the quality score for the base is not correct. In the attached example, the first read pairs are not reported even they cover the SNP, and the second read was reported but with the quality score < instead of D.\r\n\r\n## Commands\r\n\r\nextractHAIRS --bam test.bam --VCF test.vcf --singlereads 1\r\n\r\n## BAM Files\r\n7001113:798:HGCT5BCXY:1:2107:10688:87752        163     chr22   16056034        27      100M    =       16056083        148     CACTCAGCCAGTTCACCCCACCCACATTCCACAGGCTGCTTTAGGCTTTAGGACAGTGGCAAACATGGCCTCTGCCATCCCGGTCTGTGAGCGCCCCTTC   DDDDDIHIIIIIIIIIIIIIIIIIIIIIEHHIIIIHIIIIIIIIHHIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGHIIIH    MD:Z:100        PG:Z:MarkDuplicates     RG:Z:JY333     NM:i:0  AS:i:100        XS:i:100\r\n7001113:798:HGCT5BCXY:1:2107:10688:87752        83      chr22   16056083        27      99M     =       16056034        -148    AGGACAGTGGCAAACATGGCCTCTGCCATCCCGGTCTGTGAGCGCCCCTTCTTACACCAAGGTCAGTTGCTAACCAATGAGCTGCTGGGGGCCTCCTTC    IIIIIIIIIIIIIIIIHIIIGIIIIHIIIHIIIIIIHIIIIGIIIIIIIGIIIHE1IIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIGIHEFD<0DD<     MD:Z:99 PG:Z:MarkDuplicates     RG:Z:JY333    NM:i:0   AS:i:99 XS:i:94\r\n7001113:798:HGCT5BCXY:2:1213:5687:10232 163     chr22   16056108        27      98M     =       16056333        325     CCATCCCGGTCTGTGAGCGCCCCTTCTTACACCAAGGTCAGTTGCTAACCAATGAGCTGCTGGGGGCCTCCTTCTCCCACTCCCACTGCACTGTGTCC     0<D@DEEHHCDCG<CGFHD<HHHHIIIHEHHIEH@DCHEEHHIIIIIIIE?HHIIFHIEHFH?GHDHEGHHIIHHIIIEHHHHG?HGHHHIIIEHHHH      MD:Z:98 PG:Z:MarkDuplicates     RG:Z:JY333      NM:i:0AS:i:98  XS:i:93\r\n\r\n## VCF File\r\nchr22   16056126        .       G       A       198.77  PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.519;DP=23;Dels=0.00;FS=1.848;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=32.97;MQ0=3;MQRankSum=-0.228;QD=8.64;ReadPosRankSum=-0.076;SOR=0.605;VQSLOD=1.97;culprit=FS        GT:AD:DP:GQ:PL  0/1:13,10:23:99:227,0,219"},"comment":{"url":"https://api.github.com/repos/vibansal/HapCUT2/issues/comments/304155500","html_url":"https://github.com/vibansal/HapCUT2/issues/8#issuecomment-304155500","issue_url":"https://api.github.com/repos/vibansal/HapCUT2/issues/8","id":304155500,"user":{"login":"bansal-lab","id":20551613,"avatar_url":"https://avatars2.githubusercontent.com/u/20551613?v=3","gravatar_id":"","url":"https://api.github.com/users/bansal-lab","html_url":"https://github.com/bansal-lab","followers_url":"https://api.github.com/users/bansal-lab/followers","following_url":"https://api.github.com/users/bansal-lab/following{/other_user}","gists_url":"https://api.github.com/users/bansal-lab/gists{/gist_id}","starred_url":"https://api.github.com/users/bansal-lab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bansal-lab/subscriptions","organizations_url":"https://api.github.com/users/bansal-lab/orgs","repos_url":"https://api.github.com/users/bansal-lab/repos","events_url":"https://api.github.com/users/bansal-lab/events{/privacy}","received_events_url":"https://api.github.com/users/bansal-lab/received_events","type":"User","site_admin":false},"created_at":"2017-05-25T23:58:34Z","updated_at":"2017-05-25T23:58:34Z","body":"can you share the sample BAM and VCF files by email: vibansal @ cs.ucsd.edu "}}
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